TIMEOR accepts 2 input types: (1) raw .fastq files and SraRunTable (e.g. here) or a (2) RNA-seq time-series read count matrix (e.g. here) and metadata file (e.g. here).
TIMEOR is available online at https://timeor.brown.edu.
Import SraRunTable from GEO* where TIMEOR will process raw data through retrieving .fastq files, quality control, alignment, and read count matrix creation. Read this section below.
Import metadata file** and count matrix *** (skipping raw data retrieval, quality control, alignment, and read count matrix creation) and proceeding straight to normalization and correction. Read this section below.
Then simply follow the prompts. Fill out the grey boxes to begin interacting with each stage and tab.
* SraRunTable from GEO follow instructions in TIMEOR first tab (“Process Raw Data”)
** metadata file requires at least these columns. - ID, condition, time, batch - ID: a unique identifier (ID) for the user (e.g. case_1min_rep1) - condition: one word description (e.g. case, control) - time: numerical values e.g. (0, 20, 40) - batch: string description of batch (e.g. b1, b2, b3)
*** count matrix : rows should be unique gene identifiers (e.g. Flybase, Ensembl or Entrez IDs) and columns should be the IDs from metadata file.
This tutorial uses a subset of real data used in the TIMEOR publication to take the user through TIMEOR’s “Process Raw Data” tab.
This tutorial uses simulaated data and takes the user through TIMEOR’s functionality. NOTE: figures with two panels are the same page, split.